Visualising indexed and sorted bam files

Question

[YOUSEUFS]

I'm a new PhD student and bioinformatics is all very new to me so apologies if this seems trivial. I have some paired-end RNA-seq data which I've managed to convert to sorted and indexed bam files however I'm confused to where I go from here, am I right in thinking I can now visualise this data and if so how?

[mastal511]

You can use the Broad Institute's IGV to look at the data.

[GenoMax]

Follow the IGV user guide here. You need to select exactly the same genome (and its annotation) that you used for alignment of your data.

Answer 1

[GouthamAtla]

You can visualise the indexed BAMs with IGV. It should be pretty straight forward if you choose the correct genome build.

If you are working human or mouse genome, or any of the genomes listed on ucsc genome browser, you can convert your bam files to bigwig files using deepTools2 and create tracks to be viewed on genome browser. These tracks can be saved and visualised on any web browser and can be shared with collaborators.

[YOUSEUFS]

Thank you very much!

Answer 2

[Charles Plessy]

You can upload the BAM files to the ZENBU genome browser, that provides various ways to visualise the alignments.

If you want to better see the pairing relationships, you can also convert the files to the BED12 format (see pairedBamToBed12: converts paired-end BAM to BED12 format, based on bedtools), for which ZENBU also has good support.